Methods in Ecology and Evolution

Article	Citations
Generalizing hierarchical and variation partitioning in multiple regression and canonical analyses using the rdacca.hp R package	487
ENMeval 2.0: Redesigned for customizable and reproducible modeling of species’ niches and distributions	289
geomorph v4.0 and gmShiny: Enhanced analytics and a new graphical interface for a comprehensive morphometric experience	282
Predicting into unknown space? Estimating the area of applicability of spatial prediction models	189
Methods for testing publication bias in ecological and evolutionary meta‐analyses	159
Redundancy analysis: A Swiss Army Knife for landscape genomics	131
Improving Landsat predictions of rangeland fractional cover with multitask learning and uncertainty	114
Broad‐scale applications of the Raspberry Pi: A review and guide for biologists	112
Towards a more balanced combination of multiple traits when computing functional differences between species	109
rTPC and nls.multstart: A new pipeline to fit thermal performance curves in r	96
A deep active learning system for species identification and counting in camera trap images	91
SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology	89
Machine learning and deep learning—A review for ecologists	87
Deep learning as a tool for ecology and evolution	85
The Movebank system for studying global animal movement and demography	79
Generalized hidden Markov models for phylogenetic comparative datasets	76
dartR v2: An accessible genetic analysis platform for conservation, ecology and agriculture	71
Outstanding challenges and future directions for biodiversity monitoring using citizen science data	71
On the measurement of microclimate	70
Unbiased population heterozygosity estimates from genome‐wide sequence data	70
A practical guide to question formation, systematic searching and study screening for literature reviews in ecology and evolution	66
Automated detection of wildlife using drones: Synthesis, opportunities and constraints	62
Autocorrelation‐informed home range estimation: A review and practical guide	62
Spatial thinning and class balancing: Key choices lead to variation in the performance of species distribution models with citizen science data	55
The Flora Incognita app – Interactive plant species identification	53

spOccupancy: An R package for single‐species, multi‐species, and integrated spatial occupancy models	51
An assessment of minimum sequence copy thresholds for identifying and reducing the prevalence of artefacts in dietary metabarcoding data	51
Estimating forest above‐ground biomass with terrestrial laser scanning: Current status and future directions	51
ubms: An R package for fitting hierarchical occupancy and N‐mixture abundance models in a Bayesian framework	49
Acoustic indices perform better when applied at ecologically meaningful time and frequency scales	48
ALPACA: A fast and accurate computer vision approach for automated landmarking of three‐dimensional biological structures	47
track2KBA: An R package for identifying important sites for biodiversity from tracking data	47
Measuring temporal change in alpha diversity: A framework integrating taxonomic, phylogenetic and functional diversity and the iNEXT.3D standardization	46
flexsdm: An r package for supporting a comprehensive and flexible species distribution modelling workflow	45
A new joint species distribution model for faster and more accurate inference of species associations from big community data	45
Navigating the temporal continuum of effective population size	45
Meta‐analysis of primary producer amino acid δ15N values and their influence on trophic position estimation	45
RevGadgets: An R package for visualizing Bayesian phylogenetic analyses from RevBayes	43
aniMotum, an R package for animal movement data: Rapid quality control, behavioural estimation and simulation	43
Phylogenetically aligned component analysis	43
Hidden Markov models: Pitfalls and opportunities in ecology	42
Replication in field ecology: Identifying challenges and proposing solutions	42
Robust ecological analysis of camera trap data labelled by a machine learning model	42
rasterdiv—An Information Theory tailored R package for measuring ecosystem heterogeneity from space: To the origin and back	42
The potential and practice of arboreal camera trapping	41
Novel methods for spatial prioritization with applications in conservation, land use planning and ecological impact avoidance	39
Defining and evaluating predictions of joint species distribution models	39
Permutation tests for hypothesis testing with animal social network data: Problems and potential solutions	39
Harmonizing taxon names in biodiversity data: A review of tools, databases and best practices	39
A standardisation framework for bio‐logging data to advance ecological research and conservation	38
The Australian Acoustic Observatory	38
scikit‐maad: An open‐source and modular toolbox for quantitative soundscape analysis in Python	38
Unifying individual differences in personality, predictability and plasticity: A practical guide	37
metabaR: An r package for the evaluation and improvement of DNA metabarcoding data quality	36
Phylogenetic multilevel meta‐analysis: A simulation study on the importance of modelling the phylogeny	36
Unsupervised acoustic classification of individual gibbon females and the implications for passive acoustic monitoring	36
Survey coverage, recording duration and community composition affect observed species richness in passive acoustic surveys	36
PICT: A low‐cost, modular, open‐source camera trap system to study plant–insect interactions	35
phenofit: An R package for extracting vegetation phenology from time series remote sensing	35
actel: Standardised analysis of acoustic telemetry data from animals moving through receiver arrays	34
Spot size, distance and emissivity errors in field applications of infrared thermography	34
The Purr‐fect Catch: Using accelerometers and audio recorders to document kill rates and hunting behaviour of a small prey specialist	34
The unmarked R package: Twelve years of advances in occurrence and abundance modelling in ecology	33
Detection dogs in nature conservation: A database on their world‐wide deployment with a review on breeds used and their performance compared to other methods	33
The power of forecasts to advance ecological theory	32
Including intraspecific trait variability to avoid distortion of functional diversity and ecological inference: Lessons from natural assemblages	32
Convergence assessment for Bayesian phylogenetic analysis using MCMC simulation	32
ForestScanner: A mobile application for measuring and mapping trees with LiDAR‐equipped iPhone and iPad	32
Estimating encounter location distributions from animal tracking data	32
Analysing economic costs of invasive alien species with the invacost r package	32
Existing and emerging uses of drones in restoration ecology	31
graph4lg: A package for constructing and analysing graphs for landscape genetics in R	30
Nearest neighbour distance matching Leave‐One‐Out Cross‐Validation for map validation	30
An evaluation of platforms for processing camera‐trap data using artificial intelligence	30
Double‐tagging scores of seabirds reveals that light‐level geolocator accuracy is limited by species idiosyncrasies and equatorial solar profiles	29

Overcoming the pitfalls of merging dietary metabarcoding into ecological networks	29
Efficient, automated and robust pollen analysis using deep learning	29
The consequences of checking for zero‐inflation and overdispersion in the analysis of count data	29
Incorporating climate velocity into the design of climate‐smart networks of marine protected areas	29
Determination of optimal flight altitude to minimise acoustic drone disturbance to wildlife using species audiograms	29
Opportunities and risks in the use of drones for studying animal behaviour	28
A workflow for accurate metabarcoding using nanopore MinION sequencing	27
orchaRd 2.0: An R package for visualising meta‐analyses with orchard plots	27
TaxoNERD: Deep neural models for the recognition of taxonomic entities in the ecological and evolutionary literature	26
A model selection approach to structural equation modelling: A critical evaluation and a road map for ecologists	26
Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms	26
AIDE: Accelerating image‐based ecological surveys with interactive machine learning	26
Interactions in statistical models: Three things to know	26
Fine‐tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches	26
A roadmap for sampling and scaling biological nitrogen fixation in terrestrial ecosystems	25
Identifying flow modules in ecological networks using Infomap	25
Plant biodiversity assessment through soil eDNA reflects temporal and local diversity	25
Animal social networks: Towards an integrative framework embedding social interactions, space and time	25
Standardized nuclear markers improve and homogenize species delimitation in Metazoa	24
Congruence of local ecological knowledge (LEK)‐based methods and line‐transect surveys in estimating wildlife abundance in tropical forests	24
Study becomes insight: Ecological learning from machine learning	24
Using acoustic indices in ecology: Guidance on study design, analyses and interpretation	24
Marine artificial light at night: An empirical and technical guide	24
State‐space models for ecological time‐series data: Practical model‐fitting	23
A machine learning approach for classifying and quantifying acoustic diversity	23
Internet on animals: Wi‐Fi‐enabled devices provide a solution for big data transmission in biologging	23
A novel red‐edge spectral index for retrieving the leaf chlorophyll content	23
Bulk arthropod abundance, biomass and diversity estimation using deep learning for computer vision	22
Machine learning applications in river research: Trends, opportunities and challenges	22
Integrating automated acoustic vocalization data and point count surveys for estimation of bird abundance	22
Biodiversity Soup II: A bulk‐sample metabarcoding pipeline emphasizing error reduction	22
Neural ordinary differential equations for ecological and evolutionary time‐series analysis	22
bdc: A toolkit for standardizing, integrating and cleaning biodiversity data	22
Protein quantification in ecological studies: A literature review and empirical comparisons of standard methodologies	21
Why did the animal turn? Time‐varying step selection analysis for inference between observed turning‐points in high frequency data	21
Telemetry‐validated nitrogen stable isotope clocks identify ocean‐to‐estuarine habitat shifts in mobile organisms	21
A cost‐effective video system for a rapid appraisal of deep‐sea benthic habitats: The Azor drift‐cam	21
A spatial capture–recapture model to estimate call rate and population density from passive acoustic surveys	21
A guide to sampling design for GPS‐based studies of animal societies	21
Ecological inference using data from accelerometers needs careful protocols	20
mcera5: Driving microclimate models with ERA5 global gridded climate data	20
Rcompadre and Rage—Two R packages to facilitate the use of the COMPADRE and COMADRE databases and calculation of life‐history traits from matrix population models	20
Quantifying carbon in tree bark: The importance of bark morphology and tree size	20
A unifying framework for quantifying and comparing n‐dimensional hypervolumes	20
Lights, camera, pliman! An R package for plant image analysis	20
Extending Bayesian Elo‐rating to quantify the steepness of dominance hierarchies	20
treetop: A Shiny‐based application and R package for extracting forest information from LiDAR data for ecologists and conservationists	20
Revisiting animal photo‐identification using deep metric learning and network analysis	20
Recent developments in empirical dynamic modelling	20
ROBITT: A tool for assessing the risk‐of‐bias in studies of temporal trends in ecology	20
Disentangling effects of climate and land use on biodiversity and ecosystem services—A multi‐scale experimental design	20
Modelling the joint effects of body size and microclimate on heat budgets and foraging opportunities of ectotherms	20
Automated retrieval of information on threatened species from online sources using machine learning	19
Continuous‐surface geographic assignment of migratory animals using strontium isotopes: A case study with monarch butterflies	19
Optimizing aerial imagery collection and processing parameters for drone‐based individual tree mapping in structurally complex conifer forests	19
Signalling in groups: New tools for the integration of animal communication and collective movement	19
Integrated SDM database: Enhancing the relevance and utility of species distribution models in conservation management	19
A novel and efficient method for wood–leaf separation from terrestrial laser scanning point clouds at the forest plot level	19
Assessing the performance and efficiency of environmental DNA/RNA capture methodologies under controlled experimental conditions	18
rphylopic: An R package for fetching, transforming, and visualising PhyloPic silhouettes	18
Assimilate, process and analyse thermal dissipation sap flow data using the TREX r package	18
A Double machine learning trend model for citizen science data	18
Identifying direct and indirect associations among traits by merging phylogenetic comparative methods and structural equation models	18
Tracking the temporal dynamics of insect defoliation by high‐resolution radar satellite data	18
Innovations in movement and behavioural ecology from camera traps: Day range as model parameter	18
Validating ATLAS: A regional‐scale high‐throughput tracking system	18
MEDI: Macronutrient Extraction and Determination from invertebrates, a rapid, cheap and streamlined protocol	18
HumBug – An Acoustic Mosquito Monitoring Tool for use on budget smartphones	18
Terrestrial laser scanning to reconstruct branch architecture from harvested branches	18
A primer on partially observable Markov decision processes (POMDPs)	17
Estimating species relative abundances from museum records	17
Positional errors in species distribution modelling are not overcome by the coarser grains of analysis	17
A practical guide to understanding and validating complex models using data simulations	17
Infectious disease phylodynamics with occurrence data	17
Tree species classification from complex laser scanning data in Mediterranean forests using deep learning	16
Advancing diet reconstruction in fish eye lenses	16
Selection of sampling sites for biodiversity inventory: Effects of environmental and geographical considerations	16
Domain‐specific neural networks improve automated bird sound recognition already with small amount of local data	16
TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution	16
Physics‐based model to predict the acoustic detection distance of terrestrial autonomous recording units over the diel cycle and across seasons: Insights from an Alpine and a Neotropical forest	15

Fast model‐based ordination with copulas	15
Analysing individual 3D tree structure using the R package ITSMe	15
Incorporating time into the traditional correlational distributional modelling framework: A proof‐of‐concept using the Wood Thrush Hylocichla mustelina	15
Solving the sample size problem for resource selection functions	15
Shannon entropy as a robust estimator of Zipf's Law in animal vocal communication repertoires	15
The data double standard	15
Conditional repeatability and the variance explained by reaction norm variation in random slope models	15
poems: R package for simulating species' range dynamics using pattern‐oriented validation	15
Automated classification of avian vocal activity using acoustic indices in regional and heterogeneous datasets	14
Integrated population models poorly estimate the demographic contribution of immigration	14
homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes	14
Locating large insects using automated VHF radio telemetry with a multi‐antennae array	14
Instrumental variable methods in structural equation models	14
A standardised biologging approach to infer parturition: An application in large herbivores across the hider‐follower continuum	14
Worth the effort? A practical examination of random effects in hidden Markov models for animal telemetry data	14
SuessR: Regional corrections for the effects of anthropogenic CO2 on δ13C data from marine organisms	14
An automatic classifier of bat sonotypes around the world	14
maxnodf: An R package for fair and fast comparisons of nestedness between networks	14
Integrated community occupancy models: A framework to assess occurrence and biodiversity dynamics using multiple data sources	14
ngsLCA—A toolkit for fast and flexible lowest common ancestor inference and taxonomic profiling of metagenomic data	14
A Raspberry Pi‐based camera system and image processing procedure for low cost and long‐term monitoring of forest canopy dynamics	14
Population‐level inference for home‐range areas	14
Biologically inspired herding of animal groups by robots	13
Impact network analysis and the ina r package: Decision support for regional management interventions	13
Assessing the predictive power of step selection functions: How social and environmental interactions affect animal space use	13
MBHdesign: An R‐package for efficient spatial survey designs	13
bRacatus: A method to estimate the accuracy and biogeographical status of georeferenced biological data	13
AnimalTA: A highly flexible and easy‐to‐use program for tracking and analysing animal movement in different environments	13
Merging computational fluid dynamics and machine learning to reveal animal migration strategies	13
Calibration chain transformation improves the comparability of organic hydrogen and oxygen stable isotope data	13
Long‐term automated visual monitoring of Antarctic benthic fauna	13
Tropical forests structure and diversity: A comparison of methodological choices	13
allodb: An R package for biomass estimation at globally distributed extratropical forest plots	13
Classifying the unknown: Insect identification with deep hierarchical Bayesian learning	13
CollembolAI, a macrophotography and computer vision workflow to digitize and characterize samples of soil invertebrate communities preserved in fluid	13
Reflectance spectroscopy allows rapid, accurate and non‐destructive estimates of functional traits from pressed leaves	13
Dynamic visualisation of million‐tip trees: The OneZoom project	13
Stable isotope fingerprinting traces essential amino acid assimilation and multichannel feeding in a vertebrate consumer	13
Slope and equilibrium: A parsimonious and flexible approach to model microclimate	13
Sashimi: A toolkit for facilitating high‐throughput organismal image segmentation using deep learning	12
OpenSoundscape: An open‐source bioacoustics analysis package for Python	12
Migration Mapper: Identifying movement corridors and seasonal ranges for large mammal conservation	12
Scale dependency of lidar‐derived forest structural diversity	12
Estimating animal density for a community of species using information obtained only from camera‐traps	12
Fuzzy quantification of common and rare species in ecological communities (FuzzyQ)	12
Proton‐transfer‐reaction time‐of‐flight mass spectrometry (PTR‐TOF‐MS) as a tool for studying animal volatile organic compound (VOC) emissions	12
BISoN: A Bayesian framework for inference of social networks	12
Applying computer vision to digitised natural history collections for climate change research: Temperature‐size responses in British butterflies	12
A framework for quantifying soundscape diversity using Hill numbers	12
Analytical models for β‐diversity and the power‐law scaling of β‐deviation	12
Mitigating pseudoreplication and bias in resource selection functions with autocorrelation‐informed weighting	12
A critical examination of models of annual‐plant population dynamics and density‐dependent fecundity	12
Wind‐robust sound event detection and denoising for bioacoustics	11
EasyDCP: An affordable, high‐throughput tool to measure plant phenotypic traits in 3D	11
Building ecological networks with local ecological knowledge in hyper‐diverse and logistically challenging ecosystems	11
Circular–linear copulae for animal movement data	11
Linking fire behaviour and its ecological effects to plant traits, using FRaME in R	11
EcoPhyloMapper: An r package for integrating geographical ranges, phylogeny and morphology	11
A guide for developing a field research safety manual that explicitly considers risks for marginalized identities in the sciences	11
Miniaturization eliminates detectable impacts of drones on bat activity	11
A multimodel random forest ensemble method for an improved assessment of Chinese terrestrial vegetation carbon density	11
Ten (mostly) simple rules to future‐proof trait data in ecological and evolutionary sciences	11
CMRnet: An r package to derive networks of social interactions and movement from mark–recapture data	11
phenopype: A phenotyping pipeline for Python	11
Rpadrino: An R package to access and use PADRINO, an open access database of Integral Projection Models	11
Mapping forest leaf area density from multiview terrestrial lidar	11
Developing nondestructive species‐specific tree allometry with terrestrial laser scanning	11
Synthetic microbial consortia with programmable ecological interactions	11
ISSRseq: An extensible method for reduced representation sequencing	11
smartsnp, an r package for fast multivariate analyses of big genomic data	11
Multispecies site occupancy modelling and study design for spatially replicated environmental DNA metabarcoding	11
Acoustic animal identification using unsupervised learning	11
Flying high: Sampling savanna vegetation with UAV‐lidar	10
Scaling up uncertain predictions to higher levels of organisation tends to underestimate change	10
A novel fluorescence and DNA combination for versatile, long‐term marking of mosquitoes	10
iPhenology: Using open‐access citizen science photos to track phenology at continental scale	10
Acoustic species distribution models (aSDMs): A framework to forecast shifts in calling behaviour under climate change	10
Dual‐fluorescence imaging and automated trophallaxis detection for studying multi‐nutrient regulation in superorganisms	10
ENphylo: A new method to model the distribution of extremely rare species	10
Automated call detection for acoustic surveys with structured calls of varying length	10
How to measure response diversity	10
Estimating abundance based on time‐to‐detection data	10
Non‐invasive surveys of mammalian viruses using environmental DNA	10
Invasions of ecological communities: Hints of impacts in the invader's growth rate	10
Food web reconstruction through phylogenetic transfer of low‐rank network representation	10
Continuous on‐board behaviour classification using accelerometry: A case study with a new GPS‐3G‐Bluetooth system in Pacific black ducks	10
A framework for computer‐aided design and manufacturing of habitat structures for cavity‐dependent animals	10
Global positioning with animal‐borne pressure sensors	10
soundscape_IR: A source separation toolbox for exploring acoustic diversity in soundscapes	10
Using ensemble methods to improve the robustness of deep learning for image classification in marine environments	10
An optimisation approach for designing wildlife corridors with ecological and spatial considerations	10
Balancing structural complexity with ecological insight in Spatio‐temporal species distribution models	10
Deep learning and satellite imagery predict genetic diversity and differentiation	10
Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution	10
Understanding the reliability of citizen science observational data using item response models	10